[English] 日本語
Yorodumi
- PDB-5urw: Structure of the extended type VI secretion system sheath in Myxo... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5urw
TitleStructure of the extended type VI secretion system sheath in Myxococcus xanthus
DescriptorTssB, TssC, Hcp
KeywordsPROTEIN TRANSPORT / T6SS / type IV secretion / protein machine / secretion system / sheath / contractile
Specimen sourceMyxococcus xanthus (strain dk 1622) / bacteria
Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
MethodElectron microscopy (24 Å resolution / Cell / Subtomogram averaging)
AuthorsChang, Y.-W. / Rettberg, L.A. / Jensen, G.J.
CitationEMBO Rep., 2017, 18, 1090-1099

EMBO Rep., 2017, 18, 1090-1099 StrPapers
In vivo structures of an intact type VI secretion system revealed by electron cryotomography.
Yi-Wei Chang / Lee A Rettberg / Davi R Ortega / Grant J Jensen

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 13, 2017 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1May 24, 2017Structure modelDatabase references
1.2Jul 12, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8601
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
1A: TssB
1B: TssC
1C: TssB
1D: TssC
1E: TssB
1F: TssC
1G: TssB
1H: TssC
1I: TssB
1J: TssC
1K: TssB
1L: TssC
11: Hcp
12: Hcp
13: Hcp
14: Hcp
15: Hcp
16: Hcp
2A: TssB
2B: TssC
2C: TssB
2D: TssC
2E: TssB
2F: TssC
2G: TssB
2H: TssC
2I: TssB
2J: TssC
2K: TssB
2L: TssC
21: Hcp
22: Hcp
23: Hcp
24: Hcp
25: Hcp
26: Hcp
3A: TssB
3B: TssC
3C: TssB
3D: TssC
3E: TssB
3F: TssC
3G: TssB
3H: TssC
3I: TssB
3J: TssC
3K: TssB
3L: TssC
31: Hcp
32: Hcp
33: Hcp
34: Hcp
35: Hcp
36: Hcp


Theoretical massNumber of molelcules
Total (without water)1,660,86654
Polyers1,660,86654
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Polypeptide(L)
TssB


Mass: 18016.617 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus (strain dk 1622) / bacteria
References: UniProt: Q1D305
#2: Polypeptide(L)
TssC


Mass: 56188.469 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
References: UniProt: Q1D304
#3: Polypeptide(L)
Hcp


Mass: 18065.271 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
References: UniProt: Q1D303

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / Reconstruction method: SUBTOMOGRAM AVERAGING

-
Sample preparation

ComponentName: Type VI secretion system / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Myxococcus xanthus DK 1622
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategoryImaging IDImage processing ID
2UCSFTomoIMAGE ACQUISITION1
4IMODCTF CORRECTION1
11PEETFINAL EULER ASSIGNMENT1
12PEETCLASSIFICATION1
13Tomo3dRECONSTRUCTION1
CTF correctionType: NONE
3D reconstructionResolution: 24 Å / Resolution method: OTHER / Number of particles: 687 / Symmetry type: POINT
EM volume selectionNumber of tomograms: 29 / Number of volumes extracted: 687

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more